ArticleSystematic biology2022
Improving Phylogenies Based on Average Nucleotide Identity, Incorporating Saturation Correction and Nonparametric Bootstrap Support.
Article in Systematic biology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
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27 citing papers in PubMed.
- Whole-Genome Sequencing and Comparative Genomic Analysis ofVeterinary sciences · 2026Article
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- Genomic and Functional Characterization ofFrontiers in microbiology · 2026Article
- Microbial Evolution and Systematics: Archaea and Bacteria.Progress in molecular and subcellular biology · 2026Review
- Genomic-enabled classification of threeJournal of clinical microbiology · 2025Article
- EvANI benchmarking workflow for evolutionary distance estimation.Briefings in bioinformatics · 2025Article
- Rhizosphere-triggered viral lysogeny mediates microbial metabolic reprogramming to enhance arsenic oxidation.Nature communications · 2025Article
- EvANI benchmarking workflow for evolutionary distance estimation.bioRxiv : the preprint server for biology · 2025Article
- Exploration of the genetic landscape of bacterial dsDNA viruses reveals an ANI gap amid extensive mosaicism.mSystems · 2025Article
- Genomic Analysis of 96Viruses · 2025Article
- Size Distribution and Pathogenic Potential of Culturable Airborne Clostridium spp. in a Suburb of Toyama City, Japan.Microbes and environments · 2025Article
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- The unique and enigmatic spirochete symbiont of latrunculid sponges.bioRxiv : the preprint server for biology · 2024Article
- Investigating Additive and Replacing Horizontal Gene Transfers Using Phylogenies and Whole Genomes.Genome biology and evolution · 2024Article
- The Metabolism ofMicroorganisms · 2024Article
- Article
- Putative genome contamination has minimal impact on the GTDB taxonomy.Microbial genomics · 2024Article
- Uncovering the boundaries ofmSystems · 2024Article
- Update on the proposed minimal standards for the use of genome data for the taxonomy of prokaryotes.International journal of systematic and evolutionary microbiology · 2024Article
- Comparative Analyses of Bacteriophage Genomes.Methods in molecular biology (Clifton, N.J.) · 2024Article
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4 authors.
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Abstract
Whole-genome comparisons based on average nucleotide identities (ANI) and the genome-to-genome distance calculator have risen to prominence in rapidly classifying prokaryotic taxa using whole-genome sequences. Some implementations have even been proposed as a new standard in species classification and have become a common technique for papers describing newly sequenced genomes. However, attempts to apply whole-genome divergence data to the delineation of higher taxonomic units and to phylogenetic inference have had difficulty matching those produced by more complex phylogenetic methods. We present a novel method for generating statistically supported phylogenies of archaeal and bacterial groups using a combined ANI and alignment fraction-based metric. For the test cases to which we applied the developed approach, we obtained results comparable with other methodologies up to at least the family level. The developed method uses nonparametric bootstrapping to gauge support for inferred groups. This method offers the opportunity to make use of whole-genome comparison data, that is already being generated, to quickly produce phylogenies including support for inferred groups. Additionally, the developed ANI methodology can assist the classification of higher taxonomic groups.[Average nucleotide identity (ANI); genome evolution; prokaryotic species delineation; taxonomy.].
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